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2xd5

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Revision as of 15:11, 8 July 2020

Structural insights into the catalytic mechanism and the role of Streptococcus pneumoniae PBP1b

Structural highlights

2xd5 is a 2 chain structure with sequence from Strr6. This structure supersedes the now removed PDB entry 2jci. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	2uwx, 2xd1, 2jch
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Class A penicillin-binding proteins (PBPs) catalyze the last two steps in the biosynthesis of peptidoglycan, a key component of the bacterial cell wall. Both reactions, glycosyl transfer (polymerization of glycan chains) and transpeptidation (cross-linking of stem peptides), are essential for peptidoglycan stability and for the cell division process, but remain poorly understood. The PBP-catalyzed transpeptidation reaction is the target of beta-lactam antibiotics, but their vast employment worldwide has prompted the appearance of highly resistant strains, thus requiring concerted efforts towards an understanding of the transpeptidation reaction with the goal of developing better antibacterials. This goal, however, has been elusive, since PBP substrates are rapidly deacylated. In this work, we provide a structural snapshot of a "trapped" covalent intermediate of the reaction between a class A PBP with a pseudo-substrate, N-benzoyl-D-alanylmercaptoacetic acid thioester, which partly mimics the stem peptides contained within the natural, membrane-associated substrate, lipid II. The structure reveals that the D-alanyl moiety of the covalent intermediate (N-benzoyl-d-alanine) is stabilized in the cleft by a network of hydrogen bonds that place the carbonyl group in close proximity to the oxyanion hole, thus mimicking the spatial arrangement of beta-lactam antibiotics within the PBP active site. This arrangement allows the target bond to be in optimal position for attack by the acceptor peptide and is similar to the structural disposition of beta-lactam antibiotics with PBP clefts. This information yields a better understanding of PBP catalysis and could provide key insights into the design of novel PBP inhibitors.

Trapping of an acyl-enzyme intermediate in a penicillin-binding protein (PBP)-catalyzed reaction.,Macheboeuf P, Lemaire D, Teller N, Martins Ados S, Luxen A, Dideberg O, Jamin M, Dessen A J Mol Biol. 2008 Feb 15;376(2):405-13. Epub 2007 Nov 1. PMID:18155726^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Macheboeuf P, Lemaire D, Teller N, Martins Ados S, Luxen A, Dideberg O, Jamin M, Dessen A. Trapping of an acyl-enzyme intermediate in a penicillin-binding protein (PBP)-catalyzed reaction. J Mol Biol. 2008 Feb 15;376(2):405-13. Epub 2007 Nov 1. PMID:18155726 doi:10.1016/j.jmb.2007.10.066

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2xd5"

@@ Line 1: / Line 1: @@
 ==Structural insights into the catalytic mechanism and the role of Streptococcus pneumoniae PBP1b==
-<StructureSection load='2xd5' size='340' side='right' caption='[[2xd5]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
+<StructureSection load='2xd5' size='340' side='right'caption='[[2xd5]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2xd5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Strr6 Strr6]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jci 2jci]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XD5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2XD5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2xd5]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Strr6 Strr6]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2jci 2jci]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XD5 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2XD5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=S2D:N-BENZOYL-D-ALANINE'>S2D</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=S2D:N-BENZOYL-D-ALANINE'>S2D</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2uwx|2uwx]], [[2xd1|2xd1]], [[2jch|2jch]]</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2xd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xd5 OCA], [http://pdbe.org/2xd5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xd5 RCSB], [http://www.ebi.ac.uk/pdbsum/2xd5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xd5 ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=2xd5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xd5 OCA], [http://pdbe.org/2xd5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2xd5 RCSB], [http://www.ebi.ac.uk/pdbsum/2xd5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2xd5 ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 29: / Line 29: @@
 ==See Also==
-*[[Penicillin-binding protein|Penicillin-binding protein]]
+*[[Penicillin-binding protein 3D structures|Penicillin-binding protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
+[[Category: Large Structures]]
 [[Category: Strr6]]
 [[Category: Dessen, A]]

2xd5

From Proteopedia

Revision as of 15:11, 8 July 2020

Structural insights into the catalytic mechanism and the role of Streptococcus pneumoniae PBP1b

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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